This is the first in what I hope to be a series of postings. In
the series I hope to accomplish two things, establish that evolution
is an active branch of mainstream science and that there is indeed
an overwhelming amount of evidence in favor of the idea of evolution.
Note that no single post is meant to be a proof, just another piece
of evidence that supports the theory of evolution.

In the October 11th (1990) issue of Nature, Meyer et.al. present
of paper aimed at establishing if the cichlid fish species of Lake
Victoria (Africa) are monophyletic or polyphyletic. (If they all
share a recent common ancestor in that lake or came from separate
lineages that invaded the lake). In their paper they sequenced a
363 bp part of the cytochrome b gene and a 440 bp segment of
mitochondrial DNA from what is called the control region. They
sequenced these genes from several species of fish in the lake
and a few species from relatively nearby lakes.

What they found was the sequences in the Lake Victoria
species of fish were all very similar, but they were different from
the sequences of fish in nearby lakes. All the sequences are listed
in the paper.

They came to the conclusion that this indicated the cichlid
species of Lake Victoria all derive from a recent common ancestor
in the lake. They estimate the time of divergence at about 200,000
years ago based on a model that assumes mutations are relatively
constant over time. (The lake, incidentally, had been independently
dated to be 250,000 - 275,000 years old)

The News and Views section of that issue has an overview
of the paper written by John Avise. Also, the cover photo of this
issue consists of a picture of several of these fish.

This is part two in my series of postings on studies of an
evolutionary nature. As I said in part one, I have two goals in for
this series. One, to show that evolution is an accepted branch of
mainstream science. And two, that contrary to the continual assertions
of creationists, there is an overwhelming amount of data in favor of
the theory of evolution. Again, note that no single post is intended as
a stand alone proof. This post is divided into two section, an
introduction (the part you are reading) to provide a bit of background, and
the actual summary of the paper discussed.

Speciation occurs when two (or more possibly) subsets of a
formerly interbreeding population become reproductively isolated.
For many years, speciation theorists thought that virtually all
speciation occured when the two subsets of the population where
separated by geographical boundaries. (ie, the species became split
by a river, mountain range or a small group migrated out of the
main region inhabited by the species.) Reproductive isolation
followed physical isolation as the two, now separate lineages, diverged.
This could occur for many reasons, for example mating rituals grew
different or chromosome numbers changed etc. etc. In any case the
end result would be that the two lineages could no longer interbreed
if they encountered each other. (Incidentally this type of
speciation is called allopatric speciation).

A second type of speciation, sympatric speciation, occurs when
two lineages of a formerly interbreeding population diverge to the
point of reproductive isolation while still residing in the same locale.
This was first demonstrated to occur by Guy Bush working on the Apple
maggot fly Rhagoletis pomenella.

The paper I will outline here is one found in the August 9,
1990 issue of Nature. I will continue this discussion in my next post.

In the paper outlined here (Breeuwer and Werren, 1990) the
authors examine two species of wasps living sympatrically (in the
same area).

Wasps (like ants, bees and termites) are haplodiploid
organisms. In these organisms, females develop from fertilized eggs
(so there is a male and a female contribution to the genome (i.e.
sperm and egg)) while males develop from unfertilized eggs (so there
is no male contribution to the male genome).

The authors of the paper experimented with two species of
wasps, N. vitripennis and N. giraluti. They noticed that when they
crossed individuals from different species, only males were produced.
In other words, fertilization was not occuring. They found out that
this was the result of microorganisms in the cytoplasm of the gametes
destroying the males chromosomes from his sperm.

Microorganisms had been seen in the cytoplasm of the eggs of
these species, but this alone did not prove that they were the cause
of the reproductive isolation. So what they did was feed some wasps
food that contained tetracycline, which kills microorganisms, and cross
the wasps again. What they found was, in crosses in which all the
microorganisms had been killed, the two species produced both male
and female offspring. In crosses where the parents gametes still
harbored the microorganisms, only males were produced in interspecific
crosses. (Note that intraspecific crosses (matings in the same species)
always produced male and female offspring)) Therefore they concluded
that the microorganisms made it unable for the sperm from a different
species of wasp to fertilize the females egg. This worked
bidirectionally
(N. vitripennis females to N. giraluti males and N. giraluti females
to N. vitripennis males). The microorganisms did not, however,
inhibit males and females of the same species from producing offspring
of both sexes.

The authors then went on to speculate that microorganism
induced reproductive isolation may be a quick way for sympatric
speciation to occur. The paper also list some other cases of
similar events occuring in other organisms.

This is part three in my series of postings. In this post I describe
a paper presented in the July 12, 1990 issue of Nature dealing with
sexual selection in katydids (an insect). I am going to break this
up into two articles, one to outline the underlying theory and another
to describe the experiment.

The paper I will outline deals with sexual selection. It is
well accepted that the most intense competition an organism faces is
with members of its own species. Many species tend to have limited diets
and habitat requirements, and an organism must compete with members
of his own species to secure these necessities. Of primary importance,
however, is procuring a mate. If an organism fails to do that it's
genes are eliminated from the gene pool. (Note that in nature there is
never enough food, habitat and/or mates to go around. There are always
more offspring produced in a population than will be able to reproduce.)

In many (if not most) animal systems, females choose the males
they wish to mate with. Conversely, males compete for access to
females. For example many male birds defend a territory in order to
attract females. In many mammals (ie sheep) the males (rams) engage in
contests to determine which male gets to mate. Obviously the female
will choose the male who wins because her sons will then have the genes
for winning these contests and females will choose them. [as a sidenote
this kind of "logic" on the part of females can lead to what is called
"runaway sexual selection". This occurs when the traits favored by
sexual selection become linked with the genes for preference of that trait.
This can often push the system in such a way that traits with a lower
survival value are favored because their sexual attractiveness outweighs
their negative survival value. The tail of the male peacock is an
oft-cited example of this - but that's another story].

But why should females be the one's who choose? Why don't
females compete for access to males? To answer this question, Darwin
speculated that the sex that contributed more energy to the production
of the offspring would be the sex that would be able to exercise preference. His theory of sexual selection was later expanded upon by
Williams and Trivers.

In most animal systems it is clearly the female who devotes
the most energy to the production of offspring. The female gamete
(egg) is many times larger than the male gamete (sperm). In addition,
in mammals, females must carry the offspring until birth. And furthermore females of many species provide the lions share of parental
investment after the offspring has been born.

In the paper I will present in the next article the
authors experimentally test the hypothesis that the sex devoting the
most energy to the production of offspring will be the sex that exerts
a choice amongst mates.

In their paper, the authors (Gwynne and Simmons, 1990) experiment on a katydid of, as yet, unnamed species and genus. This species
of katydid was observed to be highly variable in male contribution
to parental investment. In these insects, the males transfers a spermatophore to the female after copulation. The spermatophore contains
the ampulla, which contains the sperm, and the spermatophylax, which
the female eats. The spermatophylax has been demonstrated to increase
both the number and fitness of offspring sired by the male (it is a
source of nutrition to the female).

In their experiment the authors set up two cages. In cage one
(the control) the katydids were allowed to feed on the pollen of their
host plants. In cage two the katydids were allowed to feed on the
pollen, but were also provided a nutritional supplement (the experimental cage). Therefore, in the control cage (with limited food) the
value of the males spermatophore is much greater to the female. Females
were introduced to both cages and their behavior was observed.

In the control cage (with limited food) the males exerted a
mating preference and females competed for mating opportunities
with males. This is because, with a scarcity of food, the male spermatophore became a valuable asset.

In the experimental cage, the females exerted the
mating preference because with an abundance of food, the male spermatophore was not such a valuable asset. In this way the authors
showed that (in katydids at least) the parental investment is the
determining factor in courtship roles (i.e. which sex exerts the
mating preference)

This is my fourth posting in my "evidence for evolution" series.
This will be a short one. It's a short, gee-whiz paper from Science. In
my next post (tomorrow, maybe) I'll explain a paper in Nature in which
the authors sequenced DNA from a 17-20 MY old magnolia leaf. I'll tell
what they found (it's cool) and how they did it (also cool).

In the July 13, 1990 issue of science, Gingerich et. al. report
on an interesting fossil found in Egypt. It is a whale with feet. The
skeleton is of the species Basilosaurus isis. This whale lived in
the Eocene period (in Egypt (then under water obviously)).

Current cetacea (whales), as you are no doubt aware, do not have
external hind limbs. But whales, which are mammals, evolved from terrestrial mammals. This fossil, therefore, is a link between the two. The
skeleton they show is long (16 m) and serpentine. The authors believe
this whale hunted in shallow mangrove or seagrass habitat. It's hind
limb has a short femur and a slightly shorter fibula and tibia. It
has no thumb and a greatly reduced second digit. The other three fingers are quite long (relatively). In short, another variation of the
basic mammalian leg.

The authors speculate that the limbs were tucked in close to
the body while the whale was swimming (and the topography of the
bones suggest that they are correct). Furthermore, they go on to
speculate that the limbs served as a copulatory guide for the whale.

The one thing I didn't like about the paper was a lack of
actual photographs of the specimen. They gave graphs and schematic
diagrams of all the salient features, but no photos. I would think
that in a paper of this nature, a picture would have been worth a
thousand words. Maybe they are working on the reconstruction and
want to complete it before display.

This is my fifth posting in my "evidence for evolution" series.
In this post I will explain a paper in the April 12, 1990 issue of Nature
in which the authors sequence a 17-20 million (yes, thats million) year
old DNA sequence from the chloroplast of a fossilized Magnolia plant.
I will use this post to make two points (besides the usual). One, to
explain the significance of their actual results. And two, to introduce
you to a new molecular biological technique that has opened up a vast
horizon of possible molecular evolutionary studies. The technique is
called polymerase chain reaction (or PCR for short). This first article
describes the technique. The second article will describe it's application. This article assumes some knowledge of basic molecular biology.
I give a reference for a more detailed discussion near the end.

PCR is a technique that allows a researcher to pick a region
of DNA from a very small sample and amplify it to some usable quantity.
It works by iterating cycles in which only the region of interest is
amplified.

At the beginning of a cycle the DNA is double stranded (I'll
call the strands the + and - strands). The DNA is then heated and the
strands come apart. Then the DNA is cooled. As it cools, primers bind
the DNA. These primers are short oligonucleotides chosen by the
experimenter and added to the DNA mixture at the beginning. They flank
the region to be amplified. One binds to the + strand and the other
binds to the - strand. Their 3' ends both face the region to be amplified (remember DNA is synthesized in the 5' to 3' direction) so that
polymerization can only occur in that region. A DNA polymerase then
begins adding nucleotides to the 3' end of both primers, synthesizing
a new - and + strand of the region of interest. Next, the reaction mix,
(which includes the DNA sample, the primers, single nucleotides and the
polymerase) is again heated and then cooled. This is repeated many times.

The result is the following. In the first cycle the + and -
strand serve as a template and a new - and + (respectively) copy of
the area of interest is made. When the cycle is repeated the primers
now have more sites to bind to, the original sample DNA sites and
the newly synthesized DNA sites. As the cycles continue, the number
of possible primer binding sites doubles each time. Therefore in a
short amount of time a negligible amount of DNA can be amplified to
a workable quantity. This is because the amount of templates is
geometrically increasing each cycle.

This is extremely hard to portray in words. A diagram of this
technique makes things crystal clear. Many biologists I know, including
myself, when first exposed to the idea of PCR said, "Why the hell didn't
I think of that?". It is a very powerful and elegant technique. For a
good, accessable overview (with the pictures to ram the idea home) see
the April, 1990 issue of Scientific American (p 56, The Unusual Origin
of the Polymerase Chain Reaction).

One further thing is worth mentioning. When you heat the DNA,
everything else in the reaction mix is going to be heated along with it.
At the temperature DNA denatures (strands separate) proteins from most
organisms (like DNA polymerases) also come apart. This presents a problem. Either the researcher would have to add new polymerase each cycle,
or a heat stable polymerase would have to be found. In fact, a heat
stable polymerase has been found and is used for PCR. The polymerase
is called Taq polymerase. It is call Taq because it comes from the
organism Thermus aquaticus, a bacteria that lives in thermal
vents in the ocean. Since the organism lives in water averaging close
to boiling, it's DNA polymerase is stable at these high temps. And,
therefore the Taq polymerase can be added to the reaction mix at the
beginning and will remain active throughout all the cycles.

In the paper I explain here, the authors (Golenberg et. al.,
1990) sequenced an 820 bp region (the rbcL gene) from the chloroplast
DNA of a compression fossil of a magnolia.

[A brief explanation of chloroplasts (and their DNA):
Chloroplasts are organelles found in the cells of plants. They
are the site of photosynthesis. These organelles are autonomously
replicating (i.e. there replication is not tied to the cell cycle.)
They contain their own genome, a single, circular "chromosome". DNA
sequences of their "genomes" and their autonomous nature led Lynn
Margulis to speculate that chloroplasts were once free living organisms that later became endosymbionts in other cells. She also thinks
this explains the presence of mitochondrian in cells (as well as
basal bodies). This is now generally accepted. But, that's another
story]

The fossil leaf they extracted the DNA was from a compression
fossil formed when the leaf sank to the bottom of a lake. The conditions were very anoxic (lacking in oxygen) and as a result the
fossil was in very good condition. In the News and Views section of
the same journal they show a photo of the fossil; the leaf was still
green! And, as you will see, it still contained DNA. They authors
mention that many well preserved compression fossils were recovered.
These fossils were from organisms living in the Miocene, 17 - 20
million years ago!

Anyway, the authors extracted what DNA they could from the
fossil and amplified the rbcL gene via PCR. The primers they used
were 30 bp oligonucleotides synthesized to match the sequence of
Zea Mays (corn). Since rbcL codes for a necessary protein,
ribulose-1,5-bisphosphate carboxylase, they expected the sequence to
be conserved enough for the primers to bind. It was. They also ran some
tests to insure the sequence they got was actually from the fossil
and not an outside contaminant. It was.

The sequence of the fossil and two extant species of magnolia
are given along with one other plant species. The fossil magnolia,
given the species name Magnolia latahensis, yielded a sequence
similar, but distinct from the extant species of magnolia. The
magnolia sequences (fossil and extant) formed a cluster distinct from
sequences of closely related species (tulips and petunias for example).

The authors conclude that the sequence they got was from the
fossil and that the fossil was from a now extinct species of Magnolia.

The power of this technique (PCR) suggests many applications
for evolutionary biologists. Any organism in which the tissue is intact can potentially yield enough DNA to sequence. (This includes
insects in amber, wooly mammoths and museum specimens) This knowledge
can be used to resolve phylogenies of extinct organisms. Also, if
enough samples are available, one could estimate the genetic diversity
of past populations of organisms and how it changed through time.
There has already been a paper of this nature in Journal of Molecular
Evolution. In that paper the researcher traced the genetic diversity
of Kangaroo Rats of California. Someone in my lab is doing the same
thing on an endangered species of beetle here in Massachusetts. She
is getting the DNA from pinned museum specimens that go back over
one hundred years.

In this post I present two models of sexual selection and a
paper that tests one of the predictions of both models. The first
article in the post will be an exposition of the theory and the
second article will be a discussion of the paper.

Darwin, and others, noticed that in many species males developed
prominent secondary sexual characteristics. A few oft cited examples are the
peacocks tail, coloring and patterns in male birds in
general, voice calls in frogs and flashes in fireflies. Many/most of
these traits are a liability from the standpoint of survival, mainly
because an ostentatious display to attract females is also going
to catch to the eyes/ears/nose/whatever of predators. How then could
natural selection favor these traits? Well, as I pointed out in a previous post, the sexual attractiveness of these traits outweighs the
liability incurred for survival. A male who lives a short time, but
produces many offspring is much more successful than a long lived one
that produces few. His genes will eventually dominate the gene pool of
his species.

There are two competing theories as to why females are attracted to male displays. One model, the "good genes" model, states that the
display indicates some component of male fitness. A "good genes" advocate would say that bright coloring in male birds indicates a lack of
parasites. The females are cueing on some signal, in this example color,
that is correlated with some other important trait (ex. parasite load).

The second model, proposed by Fisher, is called the "runaway
sexual selection" model. In his model he proposes that females develop
a preference for some male trait (without regards to fitness) and then
mate with these males. The offspring of these matings will therefore
have the genes for both the trait and the preference for the trait.
Note, these genes would be expressed in the males and females respectively. As a result the process snowballs out of control until natural
selection brings it into check. An example to clarify.

Suppose, due to some quirk of brain chemistry, female birds
of one species prefer males with longer than average tail feathers.
Males in the population with longer than average feather will therefore produce more offspring than the short feathered males. So in
the next generation, the average tail feather length will increase.
As the generations progress, tail feather length will increase becuase
females prefer not a specific length tail, but tails a little longer
than average. Eventually tail feather length will increase to the
point were the liability to survival is matched by the sexual
attractiveness of the trait and an equilibrium will be established. Note
that in many exotic birds male plumage is often very showy and many
species do in fact have males with greatly elongated feathers. In
some cases these feathers are shed after the breeding season.

In both of these models, which are not mutually exclusive, it
is predicted that female mating preference will be correlated with
the male trait. In the first case because the trait is a signal for
some other, underlying beneficial trait. In the second case because
the the genes for the trait and preference for the trait are, or
become linked.

In the paper I will present, the authors test this prediction.
Their paper is not an attempt to discriminate between these two models.
If the common prediction of both of these models turned out to be
false, then both the models would have to be given the boot. That is
the justification for the study.

In the paper I discuss here, the authors (Houde and Endler,1990)
conduct experiments on the guppy Poecilia reticulata. They collected
these fish from 7 different streams that harbor these species. Each
stream differed in the color pattern of male fish residing there. Male
guppies had orange coloring covering from between 5% to 17% of their body,
depending on which stream they came from.

They experimented by placing 6 males and 6 females in a tank
and measuring the sexual attractiveness of the males. This was calculated as percentage of male displays that elicited a response from
the female. In each separate experiment all the males were from one
locale and all the females were from the same or another locale. They
tested most, but not all, of the possible combinations of male/females.

They found that, female guppies from streams where males
had large amounts of orange coloring strongly prefered male
guppies with large amounts of orange to males with less orange. In
populations where males had low amounts of orange coloring the
females had no real preference with respect to coloring. The
preference exhibited by females in the first sentence was, of
course, statistically significant.

They interpreted this as, in the populations where coloring
is prominent, evolution of female preference is correlated with the
evolution of the male trait. In the populations where coloring is
less prominent, there is no association between the male trait and
the female preference.

The authors also mention a few factors that may confuse the
issue. It had previously been shown that females in lightly predated
waters favored brightly colored males more than females in heavily
predated water.

In addition, a similar experiment by Kodrick and Brown had
shown that females always prefered prominently colored males. They
point out however, that these fish were from highly inbred lab stocks
whereas Houde and Endler used fish recently sampled from nature
(all the fish were less than three generations removed from the wild).

To conclude, the authors reach the conclusion that female
preference and male trait are correlated in populations where the
male trait is prominent. This was a prediction of both the "good
genes" and the "runaway sexual selection" model.

Here's number seven in my series. It's about sperm competition and male mate choice in 13 lined ground squirrels. As I
have said before, each post is just the summary of some current
paper published in a mainstream peer reviewed journal. This shows
that evolutionary biology is a valid. productive branch of science
and is recognized as such by the scientific community as a whole.
No article is meant as a capsule proof of evolution.

In most species, females choose the males they wish to mate
with. This is not the case in the thirteen lined ground squirrel,
Spermophilus tridecemlineatus. In this system, oestrous females
mate with any male that approaches them. On average a female will
have two matings. The first male to mate will sire more of the
offspring than the second (this is due to sperm competition). The
ratio of first male offspring to second male offspring is modulated
by two factors: delay between matings and duration of second mating.
The longer the delay between the first and second mating, the less
offspring the second male will sire. He can increase this number,
however, by increasing copulatory time.

So, when a male arrives at a female who is already being
courted he has two choices. (note, the first male on the scene is
always the first to mate) He can wait until the first male leaves,
or attempt to find a new female (hopefully an unmated one). As it
turns out, females are scarce enough that it usually pays for the
second male to wait. Siring fewer offspring is preferable to not
finding a mate and siring none. However, males had been observed
in the field rejecting certain females (ones who had mated awhile
earlier) and searching for a new mate rather than going for the
sure copulation.

The authors worked out a mathematical model (a fairly
simple one) that showed, after a long enough time has passed
since the first mating, the second male is going to sire a negligible
amount of the female litter (due to sperm competition, remember the first
male sires more and the proportion gets larger as time goes on). In this
case the probability (although low) of producing offspring from an
unmated female that he still has to go locate is greater than the
probability of producing offspring from the female he has located.
(Actually it's a bit more complicated than this, but this simplifies
the picture without (IMHO) distorting it) The author calculated that
the critical time to be 3.8 hours, after that a male should reject
a previously mated female.

The authors then observed the squirrels mating and observed
that second matings did, in fact, decrease in time. They also
found that, on average, males would reject a previously mated female
if she had mated 3.82 hours earlier.

The authors concluded that, since the behavior of squirrels
closely matched their predictions. And, since their predictions were
formulated based on sperm competition; sperm competition is most
likely the factor determining male acceptance/rejection of mated
females in 13 lined ground squirrels.

In regards to my previous squirrel post (actually two), the
thought just crossed my mind that some people might get the wrong
idea (or heaven forbid want to ridicule evolution by making a straw
man of what I said) about how male ground squirrels "know" to
reject previously mated females.

First off I would like to make it quite clear that the
squirrels do not need to be trained in math to determine this. They
don't avoid previously mated females after 3.8 hours because they
understand the underlying mathematical model, but because natural
selection favors males who "know" 3.8 is the magic number. Allow
me to elaborate.

If a male happens upon a female who had mated, oh
lets say 2.4 hours previously, decides to go looking for a new
mate, (on average) he would sire less offspring than if he would have
waited. Likewise, if a male waits 5 hours after the first mating
for his chance, he will (on average) produce less offspring than had
he wandered off to search for a new mate. However, males who, for
whatever reason, go searching for mates after 3.8 hours will on
average produce more offspring than males who wait any other
amount of time. And as time goes on their offspring (who "know"
to start searching after 3.8 hours) will come to make up a larger and
larger percentage of the gene pool. Natural selection will favor
males who search for a new mate when the female they find has
mated 3.8 hours or more ago.

So males don't need to run around with calculators to
figure out how long to wait, the answer has been passed on to
them by their male ancestors who, by chance, hit upon the right
length of time.

One last question could be asked. How do males know if and
how long ago the female mated? I don't know the answer to this. Any
thirteen lined squirrel experts out there? It could be any number
of things. Even a rough estimate could be beneficial to the male.

In one of my earlier posts in this series, I presented two
(non mutually exclusive) models of sexual selection. Those were
the "good genes" model and the "runaway sexual selection" model.
Well, there is actually a third model out there also (which does
not exclude the others). I'm not aware of any name for it, I'll
just call it the "existing female preference" model. According to
this model, females have a built in preference for a certain type
of male, even if that type of male does not exist.

The paper I summarize here is in the Nov 9, 1990 issue of
Science. In the article, the author claims that, in swordfish, the
female preference for males with swords existed before males had
swords.

Within the genus Xiphophorus there are swordless platyfish
and swordtails. The swordless state is considered to be ancestral.
Basolo (the author) experimented with females of the species X.
maculatus. Males of this species are swordless. He placed a
female in the center of an aquarium that was sectioned into three
areas. On one side, he placed a normal male. On the other he placed
a male with an artificial sword attached. She noted that the female
prefered (stayed on that side of tank and offered mating displays)
the male with the artificial sword. The experiment was redone and
males switched sides (to control for side bias). The result was the
same, the female prefered the male with the sword to the swordless
male.

The author further experimented to determine if it was the
sword itself the female was cueing on. To do this she repeated the
above experiment except in this case both males had artificial
swords. One sword was colored, the other was opaque (clear plastic).
In this case the female prefered the male with the colored sword.
The control (for side preference) was also run. In addition, the
author removed the swords and switched them between males and ran the
tests (and controls) again. The results were once again, the same.
The female prefered the male with the visible sword.

So, the data she collected were. [small aside, yes the word
"data" is plural. "Datum" is the singular. Computer types simply
misused the term often enough that it has become accepted in
computer literature]

Females (from this species that had never seen males with swords)
prefered males with swords.

The females were not cueing on some side effect of the sword. (The
clear vs. colored sword showed this. One possible side effect the
female could have cued on was a unique swimming motion induced by
the presence of the sword)

The female (in the colored vs. clear sword experiment) was not cueing on some other trait of the two males. (The switching swords experiment showed this. When the swords were switched, her preference
switched.)

The author then concluded that the females in this genus have
a pre-existing preference for males with swords. It is not surprising
then that many species in the genus have swords, males have exploited
this bias. What may be surprising to some is that some species don't
have swords. This (IMHO) illustrates a pervasive misunderstanding that
most people (and sadly many biologists) have about evolution. Evolution
is not goal oriented. In this case there is no "selection pressure"
for males to develop swords. They are not being pushed to develop swords.
If, by chance, one males fins by chance happen to be longer than the
other males in his population, he will enjoy greater reproductive
success (because he is more "swordlike" than the others). This could
continue until enough mutations have been selected for that males in
this species have swords. But (and this is a very important but) there
is no mechanism that is directing this to happen. In other words, there
is no pressure on the males to develop swords. It's a fairly subtle
point that is hard for many in our culture to accept. We live in a
culture that likes to view things in terms of progress or heading
towards a goal. Evolution is neither progress nor goal oriented.

Here's a switch, I'll try posting something productive instead
of flaming people. I'll discuss here a paper in a recent issue of
Nature. The author, Lin Chao, examined the RNA virus phi 6 to see if
Muller ratchet was operating. I'll post this in two parts. In part
one I'll explain what Mullers ratchet and genetic drift is. In part
two I'll summarize the paper and explain it's significance.

H.J. Muller proposed, in 1964, one reason why sex may be
beneficial to organisms. In a strictly asexual lineage, recombination
is not possible (in sexual lineages it, of course, is). Thus, any
mutation that occurs in an asexual lineage can only be corrected in
one of two manners. The back mutation can occur or a compensating
mutation can occur. Since mutations occur at random, the probability
that the next mutation occuring in the lineage is the back mutation
is low. Thus, each new mutation the lineage absorbs is likely to be
a unique mutation. And, since mutations are most often deleterious;
an asexual lineage is expected to decrease continually in fitness.
Compensating mutations are also highly unlikely. This continual
decrease in fitness, driven by mutations, is called Mullers ratchet.
The term comes from the idea that each mutation moves the "ratchet"
one notch forward and it cannot be moved back.

Sexual lineages
have one other option to overcome mutations, recombination. If a
gene is mutated in a sexual organism, recombination can occur with
it's mate's homologous gene. Thus the offspring will have a nonmutated gene. If a sexual population has several different mutations
in various genes in it's gene pool; it is possible through recombination to reconstruct an unmutated progeny. Recombination is several
orders of magnitude more common than mutation, so it can easily
"take care of" mutations as they arise. Some (most?) biologists think
this is why sex evolved (and continues to this day). It eliminates
the operation of Mullers ratchet (because organisms can shuffle all
the "good genes" in the gene pool into one organism).

In order to understand the paper I will outline in my 2nd
post, one must understand one more concept, genetic drift. I'll
only explain this briefly.

Genetic drift is caused by a binomial sampling error of the
gene pool. In a finite population (as all biological populations
are) the gametes contributing to the next generation are a sample
of the alleles in the gene pool. As anyone who has any grasp of
statistics can tell you; the smaller a sample, the less likely
you are to get an accurate description of the population. So, in
populations that undergo a bottleneck (a severe reduction in numbers),
the sample of alleles going to the next generation is a small sample
of the population gene pool. Thus, the frequency of each allele in
the following generation will be different in the next generation due
solely to chance (binomial sampling error to be specific). [Note:
this is assuming natural selection is not operating on the allele
in question. Natural selection also changes allele frequencies.]
The greater the bottleneck, the more severe the sampling error, or
genetic drift, is. [Drift occurs to some degree in all population
whether they are bottlenecked or not. The smaller the population,
the greater effect drift as.]

Drift relates to Mullers ratchet in the following manner. When
a mutation occurs in an asexual lineage, only one organism has the
mutation. The rest of the organisms are unmutated. If the mutation is
only slightly deleterious, it can increase via drift and eventually
the unmutated version of the gene can be lossed. When this occurs, the
ratchet has clicked a notch and can't be reversed. (The unmutated gene
is lost from the population barring a back or compensatory mutation)
Of course, to strictly asexual lineages, there is no such thing as
a population. Each organism is it's own species. But, there are
precious few strictly asexual organisms in the world. Most asexual
lineages find some way to "mix and match" genes with those like
them, and (as Deaddog could attest) those not really all that much
like them. So, in that case, the population of organisms is meaningful.

In this paper Lin Chao propagated 20 lineages of the RNA
virus, phi 6. This virus was chosen for two reasons. One, it is
asexual. (Actually, it has three distinct regions that can be
recombined, but recombination can not occur within these regions.)
And two, it has a mutation rate several orders of magnitude higher
than similar DNA viruses. (In addition, DNA viruses reproduce
sexually.) All 20 lineages derived from a single parent virus.

In each lineage he subjected the virus to 40 growth cycles.
Each cycle consisted of picking a single virus and growing up a
population of 8*10^9 viruses from it. So, the virus was subjected
to 40 bottlenecks to intensify drift. If the single virus chosen
contained a mutation, the mutation could not be rectified. The
ratchet had clicked a notch. (Intensifying drift corrected for
the fact that a small amount of recombination is possible in
this virus as I mentioned before.)

At the end of the forty cycles he measured the fitness of
each of the 20 lineages (compared to the original parent virus).
(Fitness of each lineage was measured three times.) He found that
each of the 20 lineages differed markedly in fitness. One lineage
increased in fitness by 6%, all others decreased in fitness. One
lineage decreased to 28% of the parents fitness. The average of
the lineages was 78% as fit as the parent (the 95% confidence
interval did not include 1 (fitness of parent virus)).

The author concluded that the (highly significant/
P=0.0001) decrease in fitness was due to Mullers ratchet. Each
lineage continued to absorb mutations it could not repair. Of
course the 6% increase in fitness was an interesting result.
No real satisfying explanation of that was given. (If Mullers
ratchet was assumed to be operating in the past, however, one
possibility immediately springs to mind.)

The paper is (IMHO) important because Mullers ratchet
looks good on paper, but it had only been demonstrated once
before (in ciliates. Incidentally, allowing them then to have
sex stopped the ratchet.). Given that it is one of major
reasons sex is thought to have evolved, it's nice to have some
empirical evidence that the phenomena actually exists.

Larry and I recently had a flamewar, er... scientific discussion about evolution in humans. I just saw a paper concerning
human evolution in PNAS (Proceedings of the National Academy of
Sciences) and thought I would summarize it. This bears only tangentially on that discussion.

The authors of this paper (a bunch of people from Cavilli-
Sforza's lab) set out to draw a phylogeny of 5 human populations and
determine whether the differences in the populations were due to
natural selection or genetic drift. They gathered data
on 100 genetic polymorphisms from people from these 5 groups: two
groups of African pygmies, Europeans, Chinese and Melanesians. A
polymorphism is a trait (in this case a gene sequence) that is
variable in a population. For example, eye color in humans is a
polymorphisms.

Phylogenies are drawn by comparing gene sequences and
assuming that sequences more similar to each other are more
closely related than sequences less similar to each other. [For
a brief intro into the theory behind this see Li and Graur, 1991,
Fundamentals of Molecular Evolution, Sinauer. There's a little
more to it than I'm letting on. However, phylogeny construction
is (IMHO) so unbearably boring I don't want to get into the details
here.] They arrive at a tree that shows the African populations
branching off from the others about 100,000 years ago. (Estimating
time of divergence assumes a constant rate of mutation - the
relationship of the sequences do not. IMHO, it is not a great idea
to automatically assume mutation rates are constant.) Next the
Melanesian stock split off from the European/Chinese lineage. Then
the Europeans and Chinese split. Finally (in the other half of the
tree) the two African stocks separated.

This tree, however, has serious problems. I won't get into
them but basically there are a series of checks you can run to see
if the tree the computer spits out is reasonable. This tree wasn't.
For one thing the tree required Europeans to have an incredibly
slow rate of evolution compared to the other populations. The
authors find this unlikely although they add (are you out there
Larry?) that the population explosion due to the agricultural
revolution may have frozen drift and slowed evolution in Europeans by 20-25%.

Using some historical evidence the authors make the assumption
that the European stock was an admixture of two other lineages. They
then feed the numbers back into the computer and get the following
tree. The first split is again the African/others bifurcation.
Next the Chinese and the Melanesians split off. Then the European
population is formed as a hybrid of the Chinese and as yet undifferentiated African stock. Finally the two African stocks diverge. The
authors conclude this tree is more reasonable.

Next they tried to determine if the distribution of polymorphisms is due to drift or selection. They did this by calculating the
Fst value for each polymorphism. Fst values are a measure of the
variation in a subpopulation with respect to variation in the pooled
population. (For details about Fst see Hartl and Clark, 1989, Principles
of Population Genetics, Sinaeur.) They determined a distribution of
Fst based solely on a model of drift and compared that to the numbers
they calculated. They rejected the null (P=0.0023). There were too
many high and low Fst values (and not enough in the middle, therefore)
to be consistent with drift alone. Extraordinarily high values of
Fst indicate disruptive selection. Very low values indicate stabilizing
selection.

So basically the authors constructed a phylogeny of 5 human
groups they felt was reasonable and determined that some of the
differences in the gene pools of these groups was due to natural
selection. I thought the paper was pretty good although sketchy in
some portions. In any case, a reasonable preliminary data set and
interpretation.

Chloroplasts and mitochondria are organelles within eukaryotic
cells (cells of organisms other than bacteria, which do
not have organelles). These organelles have their own genetic material.
It has been shown previously that organellar DNA is much more similar
to bacteria than to nuclear DNA from eukaryotes. This, and other
evidence, led scientists to the now widely held belief that
these organelles were once free-living prokaryotic cells that
began living in proto-eukaryotic cells and eventually the two types of
cells required each others presence for existence. They were
obligate endosymbionts. It's worth noting that organelles
still reproduce autonomously within eukaryotic cells.

Recently, a paper in Nature provided evidence for a double
endosymbiotic event in cryptomonad algae. Several lines of evidence
led researchers to conclude this double event had taken place. First,
most chloroplasts are double-membraned (one membrane from the protoeukaryotic cell, one from the endosymbiont bacteria). Chloroplasts from
cryptomonad algae have more than two membranes. Also, these chloroplasts contain what is called a nucleomorph, a DNA containing
structure thought to be the vestige of a eukaryotic nucleus. (Prokaryotes and organelles don't have a membrane bound nucleus, their DNA
just "floats free".)

The clincher came when the researchers amplified
up regions of the 18S rRNA gene (using PCR). They found two different
length sequences that they called Nu and Nm. Nu they believe to be from
the nuclear DNA of the algae and Nm from the nucleomorph (they are
still trying to get rigorous proof of this.) The two sequences were
very divergent. The Nu was similar to nuclear DNA from amoeboid
protozoans and the Nm sequence is similar to red algae. The authors
conclude that cryptomonad algae is a chimera of two endosymbiotic
events. First a endosymbiotic event in which red algae was formed,
then this eukaryotic red algae being taken into a protozoan creating
the crytomonad algae.

Hey everyone! Here's post number nine in my series. In this
one (which should be short) I summarize a couple of paleontological
papers. Since I'm not a rockhunter myself, I won't give too much
detail.

The first paper is a report from Science by Jeram, et. al. In it
they describe fossils of land animals from the Silurian. They found an
arachnid (spider) and two centipedes. The kicker of the paper was that
land was not supposed to be colonized by animals by the Silurian. But,
finding predatory arthropods indicates a stable ecosystem containing
animals much sooner than expected. [Aside to the good guys; isn't it
nice to have a theory that is enriched, rather than embarrassed, by
new data] This finding even made it's way to the popular press, my
mom sent me a newspaper clipping (probably KC Star - I can't remember)
about it.

The second paper appeared in Nature and was authored by Pilbeam et. al. In this paper they describe two recently found Sivapithecus humeri and they discuss the hypothesis that it was closely
related to the genus Pongo. The upshot of the paper is, previous
skull specimens of Sivapithecus indicated that it was probably
closely related to Pongo, however, the newly found humeri are
not at all similar to Pongo The authors conclude that the data
is not sufficient to make a decision at this time.

If you want the full, gory, jargon-laden description, plus
the photos of these fossils check out the refs. There is also an
article about evolution of arthropods in that same issue of Science,
but it's not really that interesting (to me at least).

Well, I haven't heard any creationists on this board claim
recently that there is no evidence for evolution, but I'll keep this
series going since all the mail I've got concerning it has been
favorable. I'll summarize here a paper from the most recent issue
of Science.

In this paper, Turlings, et. al. investigate the interactions
of corn plants, caterpillars and parasitic wasps. The wasps parasitize
the caterpillars that, in turn, eat corn. The authors found that corn,
when eaten by caterpillars, releases chemicals (terpenoid volatiles)
that attracts wasps.

To determine what stimulus caused the release of these
chemicals Turlings tested the following leaf types with respect to
their ability to attract wasps: 1) leaves that caterpillars had
eaten 2) leaves that were mechanically damaged (cut w/ razor blade)
3) leaves with caterpillar saliva on them. Note that the first
type of leaf would have both mechanical damage and caterpillar
saliva on it. It had been previously established that wasps were
attracted by terpenoids.

The authors found that the first type of leaf (caterpillar
chewed) attracted the most wasps. They concluded that a combination of
damage and saliva were required to efficiently attract wasps.

In addition to measuring wasp attraction, they analyzed the
chemicals released by the corn by gas chromotography. This was to insure
that terpenoids were indeed being released. They were, so Turlings concluded
it was the terpenoids that was attracting the wasps (and these terpenoids
were only produced in response to caterpillar damage).

It had previously been shown that plants produce chemicals
to ward off grazers. Most of these chemicals, however, work in a
straightforward fashion. Bug eats chemical; bug dies. This is one of
the first papers to demonstrate a chemical defense that works in a
more roundabout way. Bug eats plant. Plant releases wasp attracting
chemical. Wasp eats bug.

The authors do not discount the possibility that the terpenoids
may also harm the caterpillars in some direct way. But, the primary
value of the terpenoids to the corn is its ability to attract a
predator of the caterpillar. There is more to the paper, but I
just wanted to hit the highlights.

In the recent Nature there are a couple of very interesting
articles (about wrens). I'll try to get around to summarizing them
this week sometime.

If you are wondering what this has to do with evolution ask
yourself this question, how did this system arrive at this point?
Remember Steve Timm claimed that creationists (some? most? all?)
believe that before "the fall" there were no predators.

It is easy to construct a plausible way for this system
to reach the point it is now at given evolutionary theory. I don't
see how you can given a creationist scenario. Both the corn and wasps
must change in the interim between the supposed fall and present time.
Creationism provides no mechanism for change.

6) "Though evolution has been studied for years, scientists have never
observed a single species evolving". So what? Evolution has been studied
for just over a hundred years. Speciation takes *LONGER* than just over
a hundred years. If you just study evolution for about a hundred years,
all you would expect to see is microevolution within species, and perhaps
the splitting off of subspecies who might be on the road to speciation.
Scientists *have* observed both of these events.

Creationists seem to want to define species evolving solely
in terms of speciation. Microevolutionary change doesn't seem to
fit their bill as evolution. In fact I just responded via email
today to some guy who didn't understand how the English moths
had anything to do with evolution. (To be fair, I'm not sure if
he was a creationist or just didn't get my point.) As Kathleen
pointed out, evolution has been observed (microevolutionary
changes and the beginnings of speciation). Most creationists (as
well as many evolutionists, perhaps) would be surprised to know that
speciation has been observed!

In the genus Tragopogon (a plant genus consisting mostly
of diploids), two new species (T. mirus
and T. miscellus)
have evolved. This occured within the past 50-60 years. The new
species are allopolyploid descendents of two separate diploid
parent species.

Here's how it happened. The new species were formed when
one diploid species fertilized a different diploid species and
produced a tetraploid offspring. This tetraploid offspring could
not fertilize or be fertilized by either of it's two parent
species types. It is reproductively isolated, the definition of
a species (well, the most common definition, at least.) The
paper I have corresponding to this are great. One new species,
T. mirus has arisen at least three separate times.

So, speciation has been observed in case they bring up
that again. In fact, it happened instantly in this case. Plants
are amazingly plastic in regards to genetics, so it really isn't
all that surprizing that the first (as far as I know) observed
speciation event would be something like this in plants.

I've mentioned the term exon shuffling in several of my
posts, so I might as well get around to explaining what the hell
I'm talking about. This is especially true since there is a paper
in this weeks Science about the "Exon Universe" that will be the
second part of this article. In this introduction to the paper,
I'll explain a little about gene structure and what exon shuffling
is. (Keep in mind that DNA codes for RNA which codes for protein)

The bacteria E. Coli was used in most of the very first
molecular genetics experiments. When the first genes were sequenced
from it, it was found that all the information for the protein
lay in one continuous stretch (an open reading frame (ORF)). It
came as a bit of a surprise when the first eukaryotic genes were
sequenced and this was not the case. It seemed typical eukaryotic
genes contained several open reading frames of DNA interrupted by
sequences of DNA that did not code for anything. The coding regions
were dubbed exons and the intervening sequences were dubbed introns.

It was soon found out that exons commonly coded for a
functional domain or subunit of a protein. In other words, that
introns often separated useful "building blocks" of proteins. Of
course this led to speculation that, perhaps exons could be
duplicated, deleted or "mixed and matched" from an existing gene
to create a whole new gene with a new function. If a whole gene
was duplicated for instance (this is fairly common), one gene
could continue doing its job while the other is free to evolve a
new function by swapping exons with other duplicated genes. This
is what exon shuffling refers to.

Of course, this would be a great way to gain new useful
genes and their corresponding proteins in a hurry. And, it wasn't
too long before exon shuffling was confirmed to have happened.
Two genes, low density lipoprotein (LDL) receptor gene and the
epidermal growth factor (EGF) were shown to be mosaic genes. Although they were functionally unrelated, they shared a few common
exons.

It may seem a bit farfetched to those who don't know much
about molecular genetics that exons could just whiz all over the
genome and conveniently plunk down in a useful place. In fact there
are plenty of mechanisms for moving DNA from one part of the genome
to another. I'll mention a couple.

One is gene conversion. This is a phenomena by which one
stretch of DNA "erases" another stretch and copies itself in it's
place. The mechanism is well known, but I don't have time to
explain it. Any molecular bio text will have that info.

Another is transposition. This is when a stretch of DNA
simply excises itself from one part of genome and moves itself
to another. Transposons are pieces of DNA that do this. Many
biologists (including myself) tend to think of them as molecular
parasites. They don't do any good to the cell or organism. But
since they move around the genome so much, it's hard to get rid
of them. Transposons carry a few genes with them, usually only the
genes required for their own movement.

If two transposons surround a stretch of DNA, they can
carry that stretch of DNA along next time they both move if they
move as one big unit.

These processes aren't directed or cognizant in any way, so
an exon doesn't know to get shuffled to the right place. In fact,
often an exon (or transposon) will plop down in the middle of a
functional gene. The result is one dead organism. But, occasionally
a good rearrangement will take place. It's a hit or miss phenomena.

So, theres an explanation of exon shuffling and a bit of
info as to how it could happen. Tomorrow, I'll try to post a
summary of the paper in Science.

O.K., here's a summary of the paper. It's not that long really,
but very dense. I'll summarize the high points and just warn you that
I'm leaving out some stuff.

The paper is called "How Big is the Universe of Exons". Recall
that an exon typically encodes on functional domain of a protein (for
example a DNA binding domain). Duplicate genes can "swap" introns
and quickly evolve new proteins. A homologous DNA binding exon, for
example, might be found in many entirely unrelated gene, indicating
it was imported intact from another gene. This "prefab" construction of genes is called exon shuffling.

The authors of the paper made the following assumption in
the beginning of the study. Since introns (the sequences that intersperse between exons) are found in all eukaryote taxa and
they typically are in the same place in homologous proteins, the
intron/exon structure of genes must be ancestral. The competing
point of view is that introns are rather new and spread through
all taxa as transposon-like elements. Some intron placement lends
credence to this view, but, IMHO, most introns were probably
present in the progeonote (latest common ancestor to all living
organisms). Some introns invaded later. As an aside I will mention
that bacteria do not contain introns, some biologists take this to
mean that they "dropped" their introns to streamline their genomes.
Others take this as proof that introns invaded after the divergence
of prokaryotes and eukaryotes. For what it's worth, I favor the
first hypothesis.

The authors then set out to calculate how many exons would
it take to account for all the proteins we have in all organisms
today. This assumes modern day proteins did not each evolve slowly
but were assembled by throwing together domains until something
worked.

To do this they plugged their computer into the Genbank and
EMBL databases and basically looked at every gene ever sequenced
(a bit of an exaggeration). They then went through and narrowed the
list of sequences down to non-homologous genes and non-homologous
sequences within genes. For example, if the alcohol dehydrogenase
sequence from one species was used, the sequences from other
species were thrown out. Likewise, if a gene had more than one
domain that was identical (not uncommon) the "extra" domains were
deleted. All this was done in an attempt to eliminate duplicate
exons from known homologous sources. (Note: all sequences were
first "transcribed" from DNA sequences to amino acid sequences
via the universal genetic code - this was done by computer)

Much mathematical/statistical/computer simulation mayhem
followed 8-) I'll supply the reference for those who want to wade
through the gory details. (I'm still mulling over some of the
analysis) Basically, however, what they did can be explained as
followed. From the sample of genes they took out of the database,
they made pairwise comparisons and checked how many identical exons
they had. They used this sample number as an estimate of the total
of identical exons in the population (all organisms). They concluded
that between 1000 and 7000 exons were needed to create all the
proteins we see today. A rather small number, all things considered.
(Boy, don't you love hand waving. I think I almost broke my wrist 8-)
At least now I understand the appeal of creationism ;-) )

At the end of the paper a considerable amount of time is
spent examining all the possible assumptions and consequent errors
that could be included in the study. They are rather numerous, but
the authors do their best to deal with them. They range from the
chances of forming two identical exons by chance to homologous
exons diverging in amino acid sequence, but not function. Some
problems would cause the estimate of total exons too small, others
would cause the number to be too large.

Well, it certainly was an interesting paper; I'll give them
that. And, I would guess that they are probably not off by too many
orders of magnitude 8-)

This is number 13 in my series of postings about current
research in evolution. I'll summarize two papers from a recent
issue of Science, both of which basically reported the same
finding. I'm kind of pressed for time today, so this will be a
bare bones summary. But, as always, I'll supply the references.

First a bit of background. In eukaryotes, (basically all
organisms except bacteria) genes typically are not found as
a single uninterrupted reading frame. There are sequences interspersed within the coding region of genes. They are excised
after the DNA is translated into RNA. These excised DNA sequences
are called introns (the coding DNA sequences are called exons).

In the two papers I will summarize, the authors present
evidence of an ancient origin for introns.

According to the endosymbiotic hypothesis of eukaryote
evolution, modern day chloroplasts are the descendents of ancient
cyanobacteria. These cyanobacteria were engulfed by an ancient
cell and a symbiotic relationship was established such that the
cyanobacteria simply continued to live inside the engulfing cell.
There are also free living cyanobacteria alive today. The authors
of the papers document the presence of an intron in a gene of
both modern day cyanobacteria and chloroplasts. In both cases
this intron is the same type in all the genes looked at (it is
a group I intron) and it is also in the same position. They
argue that this implies the intron was present in the gene before
ancient cyanobacteria split into its two present day lineages
(modern cyanobacteria and chloroplasts).

In the first paper the authors document a group I intron
in the same position in the leucine tRNA gene in two species of
Anabena (cyanobacteria) and in the chloroplasts of several land
plants (bean, liverwort, maize, rice and tobacco). In the
second paper the authors (a different bunch of fellows) show
a group I intron in the leucine tRNA gene in five species of
cyanobacteria and many chloroplasts from very different plants.

From these data the authors (in both papers) argue that this
is evidence for the intron predating the split of modern cyanobacteria and chloroplasts. If the common ancestor of these two groups
(ancient cyanobacteria) had this intron in that position, it's
current distribution can be explained by simple inheritance; both
lineages retained it. The alternate explanation would be that the
intron invaded all these lineages. Group I introns are mobile in
some lineages; they can excise themselves from one stretch of DNA
and insert themselves in another. However, it is highly unlikely
that the same type of intron would plunk down in the same spot in
all these genes. The first hypothesis (the intron was in the
common ancestor) is, IMHO, much more likely.

This is part 14 in my series called "evidence for evolution".
For Bob's benefit, I'll explain what this is about. In this series
I post summaries of recent scientific papers about evolution. I
choose the papers from mainstream, peer reviewed scientific
journals (not Evolution or Journal of Molecular Evolution or
any of those journals). This is to demonstrate that evolutionary
biologists meet the criteria of scientific worth as judged by
scientists in other fields. (As an aside, Nature publishes
about one to two evolution papers per week. I have never seen
a creationist paper presented there.) No single post is meant
to be a capsule proof of evolution. Each is merely more evidence
that it did, and does, occur. In addition, I have been chosing
papers that have come out recently. This is not a compendium of
classic papers, but rather stuff on the cutting edge.

I'll summarize here a paper that demonstrates evolution
occuring in a laboratory situation. It appeared in a recent
issue of Science [1].

In almost all dioecious species (species with two sexes),
the sex ratio is 0.5. There are 1/2 males and 1/2 females. In most
species,the Mendelian rules of inheritance explain mechanistically
why this is so. For example, in humans the offspring from any one
mating has a 50 percent chance of being male or female. This is
because the male sperm has a 50 percent chance of containing a
Y chromosome and a 50 percent chance of containing an X chromosome. Female eggs only contain X chromosomes. Individuals that
are XX are female, individuals that are XY are male. Given any
initial sex ratio, the next generations sex ratio will be 0.5.
(the proof is left as an exercise to the reader) The only exception to this would be a sex ratio of 1 or 0. An all male or
all female population has no hope of regaining a balanced sex
ratio.

The question can be asked, is the sex ratio then just a
non-adaptive consequence of the independent assortment of X and Y
chromosomes in male sperm? Or, is the ratio adaptive and Mendelian assortment an adaptive trait that has evolved?

The authors of a recent paper put this to the test by
studying the Atlantic silverside fish Menidia menidia. This
fish has an unusual life cycle in that, during the early months
of the year mostly female offspring are produced. In the
summer months mostly males are produced. The bias in the sex of
the offspring is induced by the water temperature. Female offspring
are produced while the water is cold, males while it is warm.
The sex ratio across the whole year balances out to 0.5. This
sex bias is caused by temperature dependent sex determination,
not temperature dependent sex mortality. In other words cold
water makes baby female fish form, it doesn't kill male baby
fish. The same embryo could be male or female depending on
the temperature it is raised at (i.e. Mendelian segregation does
not influence the sex ratio in this species.)

The authors captured hundreds of these fish and maintained
them in aquaria for five to six years. Some aquaria were maintained
at low temperatures, others at high temperatures. In the low temp
aquaria, the populations began with mostly females. The sex ratio
, for example, in one low temp tank was 0.70 (70% female) In the high
temperature aquaria, the populations began with mostly males. In
one of the low tanks the sex ratio was 0.18. Both of these, given
the population sizes, are significantly different than 0.50.

As the experiment progressed, the sex ratios changed
from the highly skewed initial conditions. In all the populations
the sex ratios converged on 0.5. The trajectory of the sex
ratios converging on 0.5 differed between many of the tanks.
In one tank, the next and all subsequent generations were at an
0.5 sex ration. In another, it slowly converged upon 0.5. In
yet another it reached 0.5, then overshot slightly, then
returned. This indicates that a sex ratio of 0.5 is somehow
adaptive (there is a lot of theory as to why this may be - I
may bore you with it later some time) because the fish evolved
from a skewed ratio to a balanced ratio. Since chromosome
assortment does not determine sex in these fish (temp does),
the only explanation for their convergence to 0.5 is natural
selection favored fish that produced an abnormal amount of
the minority sex. (If males are lacking, any fish that produces
male fish will contribute more than average to the gene pool).
This is a frequency-dependent kind of selection. As the sex ratio
approaches 0.5, fish who produce a disproportionate amount of
either sex will contribute less than average to the gene pool.

Finally, notice that evolution has occured. The experiment
started with populations of fish that produced skewed sex ratios
and ended with populations that produced balanced sex rations.
Since the environment was held constant, the change in the populations was therefore genetic. In other words, the gene pool
changed over time. This is the definition of evolution.

Of course, the authors were mainly concerned with the
result of sex ratios apparently being adaptive and did not
make much ado about evolution being shown to occur (for much
the same reason that modern astronomers don't constantly
stress, or try to prove, the earth is round). This is only
one of many papers actually demonstrating evolution in the lab.
There are also many demonstrating evolution occuring in the
wild (any evolution text can provide these refs - or email me
if you are interested). Also, as I have posted before, speciation
has also been documented to occur (I'll supply these refs [2,3])

This will be short as I am just taking a quick study break.
Steve Watson kindly provided us with some info as to what the
creationists are up to these days. Here's a look at what a couple
of biologists have been up to recently.

A lot of "armchair evolutionary" explanations of complex
traits follow the "little trait becomes a big trait" mode. In other
words the complex trait begins as a barely functional abnormality
and is gradually shaped by selection into a fully functional bit
of morphology (or behavior or biochemistry). These "just so" stories
are usually, however, completely unsupported by data (but, they aren't
refuted either).

The authors in the paper I'll summarize briefly here add some
weight to one "little trait becomes a big trait" explanation. Benkman
and Lindholm studied the red crossbill (Loxia curvirostra) to
examine how this birds strange bill evolved. The crossbill, as it's
name implies, has a crossed bill. The lower bill curves to one side
and the upper bill curves to the other. The unusual bill shape helps
these birds extract seeds from pine cones.

Bird bills, like human toenails, can be clipped without
injuring the organism. And, again like toenails, they grow back.
The authors used nail clippers to trim the beaks of the birds
in such a way that they were not crossed. It took about 36 days
for the bills to grow back from an uncrossed state to a crossed
state. The authors used this bill growth to mirror the probable
phylogenetic change from uncrossed to crossbilled birds.

The authors first separated the birds into a control and
an experimental group. They then measured how long it took the
birds in each group to extract seeds from a cone. Both groups
were statistically the same. They then clipped the beaks of the
experimental group and measured, over a 36 day period, how long
it took each group to removed seeds from a cone. As you would expect,
the control group did not change throughout the experiment since
it remained unaltered. The experimental group, however, did change.
In the first day after clipping it took an average of 5.28 seconds
for a bird to get at a seed. This was up from 1.34 seconds prior to
clipping. As the experiment went on, the birds got better and
better until at 36 days it took them only 1.68 seconds to get
a seed (statistically not significantly different from 1.34).
This increase in seed gathering seed was interpreted as a function
of bill crossing. The authors concluded that the crossbill trait
was selected every step of the way from an uncrossed ancestor,
because as the bill became more and more crossed, the birds
ability to quickly secure food increased. They also noted that
slight bill crossings have been sighted in straight billed
species of birds.

John Krebs (in the accompanying "News and Views" article)
notes that the paper does not address the changes in musculature,
tongue morphology and behavior that must accompany the change
in bill morphology. But, he notes that these birds provide a
very interesting avenue with which to pursue questions of this
type.

He also notes that, according to legend, these red crossbills
got their beaks crossed trying to remove the nails from Jesus Christ's
cross. The red coloring of the males symbolized his blood. For some
reason, I like the first explanation better 8-)

Well, there you have it. A short "gee-whiz" paper from
Nature. I sort of liked it (it had a good beat and I could dance
to it). Usually I don't buy these "little trait becomes big trait"
arguments, but in this case at least there is a little data to
back up the claim. (I should point out, before Larry accuses me
of being a saltationist ;-), that I'm not implying that complex traits
appear fullblown in "hopeful monsters". I just I think that it is
often the case that the current utility of a trait has little or
nothing to do with it's ancestral utility. Many complex traits may
be exaptations, not adaptations.)

Reference

Benkman and Lindholm, 1991, The advantages and evolution of a
morphological novelty, Nature 349: 519-521

Ted, in his own charming way, has explained that all science
is bogus because it is based on false assumptions and that scientists are so caught up in the momentum of what they are doing, they
can't go back and correct their "errors" (apparently this would
involve forgetting mathematics and selectively reading old manuscripts). In any case, what gets done can't be undone (ITHO). This brings
me to a recent paper in Nature. First, a little bit of ecology/evolutionary theory.

Mimicry is the phenomena of two (or more) species
looking/sounding/smelling/whatever like each other. There are two
types of mimicry: Batesian and Mullerian (should be an umlaut over the
u).

Batesian
mimicry is when one species evolves to mimic a second species that
has some trait that makes it undesirable to predators. For instance,
a butterfly that tastes good, but mimics a butterfly that tastes
bad, may evade predation as long as bad tasting butterflies outnumber
good tasting ones (it's a frequency dependent kind of thing). The
palatable species benefits because it gains the reward of looking
like a bad tasting species, but it doesn't pay the price; chemical
toxins are costly for an animal to produce. If the palatable species
becomes too numerous, the unpalatable species may suffer as
predators may learn that organisms that have that pattern/coloring/sound/smell are O.K. to eat.

Mullerian mimicry is when two (or more) foul species evolve
to look/sound/smell/whatever like each other. They both/all benefit
because predators have only to learn one signal to discriminate species
to avoid, instead of having to learn separate cues for each foul
species. This is a benefit to the prey (only coincidentally a benefit
to the predator) especially if the two (or more) mimetic species occur
at low densities.

One of the classic example of Batesian mimicry has been
the viceroy butterfly. Biology texts explain that this butterfly
is a palatable mimic of two species of noxious butterflies, the
monarch and the mueen. A new paper in Nature suggests that the
viceroy tastes every bit as bad as monarchs and worse than
queen butterflies. The authors conclude that the mimicry is a
three way Mullerian mimicry instead of the viceroy being a Batesian
mimic to the two Mullerian mimics, the monarch and queen.

Their experiments consisted of capturing 16 red winged
blackbirds from nature and offering them butterfly abdomens and
recording the response. Only abdomens were offered so that the
bird could not tell species apart by subtle changes in wing
color or morphology. Each bird was offered 8 viceroy, 8 monarch
and 8 queen butterfly abdomens dispersed at random between 24
palatible control abdomens. The percentage of each abdomen type
eaten was recorded as well as mean manipulation time and a
mean response score. The response score was basically an
arbitrary scale ranging from the bird ignoring the abdomen (0),
through pecking once (1), partially eaten (2) to completely
eaten (3). The results were as follows:

98% of the control abdomens were consumed by the birds,
68% of the queen, 41% of the viceroy and 46% of the monarch.
The monarch and viceroy scores did not differ significantly;
the other two classes did.

Mean manipulation time for the control abdomens was
5.3 seconds. For the other species it was: queen = 17.5 s,
viceroy = 23.5 s and monarch = 31.3 s. The monarch and viceroy
were again not significantly different. In addition the viceroy
was not significantly different than the queen. The monarch
and queens did, however, differ significantly.

Finally, the mean response score for the controls was
2.98. The queen, viceroy and monarchs scored 2.50, 1.98 and
2.10, respectively. In this case the viceroy and the monarch
were the only two classes that did not differ significantly.

So, all three species were significantly less palatable
than the controls. And, in two of three measures the viceroy
and monarchs were (as a class) less palatable than the queen.
This shows that the classic example of Batesian mimicry is
actually a case of Mullerian mimicry. It also disproves Ted's
notion that once science gets done, it cannot get undone.

This is my favorite kind of science paper, one in which
something widely held is demonstrated to be just plain wrong.

Reference

Ritland and Brower, 1991, The viceroy butterfly is not a batesian
mimic, Nature 350: 497- 498

Postscript:

Batesian and Mullerian mimicry involve interspecific interactions.
Intraspecific (within a species) Batesian mimicry has also been
documented. Monarchs obtain their toxins by sequestering cardiac
glycosides of their host-plant, the milkweed. In large flocks(?) of
monarchs there are many that have not spent the energy to sequester
these glycosides; they are getting a "free ride". These monarchs
can then invest more energy towards raising offspring than the
monarchs who "play fair" and spend energy to harbor the poisons.

In the marine isopod Paracerceis sculpta, there are three
discrete male morphologies. These are determined by a single allele
change at one locus. The largest of the three males, the alpha males,
defend harems of isopod females. The intermediate size male, the beta,
mimics female morphology and behavior and the gamma males, the smallest
of the three morphs, attempt to hide in large harems and not attract
the attention of the alpha male(s). The larger the male, the slower it
matures. But larger males, although they reach reproductive age later
in life, live longer and therefore have more reproductively active
years. In the paper I will summarize here, the authors demonstrate that
each male morph enjoys equal mating success.

Male reproductive success in these isopods depends on many
factors. Each male morph is able to sire roughly the same amount
of offspring when isolated from other males. Differences in male
reproductive success occur when males are mixed in the mating
area, the spongocoel. For example if the spongocoel contains one
alpha and one beta male, the beta males sires 60 percent of the
offspring. If there is one alpha and a gamma male, the alpha sires
92 percent of the offspring. If there are 2 alpha males and three
gamma males, each gamma males sires 33 1/3 percent of the offspring.
The authors give mating success for 14 different combinations of males
in the paper (all the combinations they found in nature).

They sampled isopods from a natural population for a period
of two years. They found that each male morph had, on average, equal
mating success and the alleles that determined male morphology were
in Hardy-Weinberg equilibrium (HW equilibrium is a measure of how
alleles are distributed in a population.) In the paper they present
a table showing how many spongocoels were sampled with respect to
each different combination of males. The table also lists how many
females were in each harem. To make a long story short: the numbers
of males, combinations of males and numbers of females added up
such that each male morph was equally reproductively successful.
Below is a summary of some of the data:

Although it appears alpha males have a higher mean # of
mates, the difference is not significant (look at the standard
errors in the beta and gamma males). Notice also that equal
repro success does not mean equal frequency in the population;
it only means that each male type is able to keep replacing itself
in the population. In other words, if conditions stay the same,
the ratio of alpha to beta to gamma males will stay 452:20:83.

There has been a small amount of discussion about what is a
species here on t.o (and also sci.bio) recently. A recent paper in
Nature presents some interesting food for thought on this topic.

Wayne and Jenks, in a recent Nature, present a study of the
mtDNA(mitochondrial DNA -- it's maternally inherited) of the
endangered red wolf, Canis rufus. This species, once extending
over a large range in the southeast, is now extinct in the wild. The
authors examined the mtDNA sequence of red wolves (zoo animals and
from DNA obtained from museum pelts from 1905 to 1930) as well as grey
wolves and coyotes. (The red wolf occurred only in regions where grey
wolves and coyotes were.)

When they analysed the red wolf sequences, they found that
the mtDNA was either of grey wolf type or coyote type. This (along
with the geographic information) lead them to conclude that the
"species" red wolf is (was) actually a hybrid of the grey wolf and the
coyote.

But wait, the story gets even more interesting. Grey wolves and
coyotes have overlapping ranges in the northern US, but the red
wolf phenotype is not present in hybrids in the north. The red
wolf phenotype is not only a product of the hybridization, but of
environment as well.

That's just the beginning, however, the red wolf was classified
as an endangered species; but US Fish and Wildlife does not extend
endangered species classification to hybrids. The authors argue,
however, that the "species" former prominence in the food web --
it was the top predator in it's former range -- and the possibility
that the phenotype might not be recoverable by future hybridizations
-- remember, it doesn't work up north -- indicate that the red wolf
deserves to remain classified as an endangered species.

Two new papers examining the phenomena of directed
mutations have recently appeared in the literature. I'll
quickly review these experiments in the next post. This
post is a short introduction to a few of the classic papers
relevant to this issue.

In 1943, Luria and Delbruck did an experiment that led
biologists to believe mutations occured at random. They started
many parallel cultures of E. Coli., let them grow, then exposed
them to the bacterial virus lambda. They found that the distribution of resistant cells across all the independent lines was
Poisson. Some cultures had many resistant bacteria, others had
few. If the phage had induced the correct mutation to occur,
each independent line should have roughly the same number of
mutants (a Gaussian distribution would be found across all
cultures). [1]

Lederberg and Lederberg, in 1952, provided another
experiment showing that mutations occured randomly. They grew
bacteria on plates and used round pieces of felt to transfer
bacteria to a replica plate. So, the pattern of colonies growing
on the two plates were identical -- and the corresponding colonies
on each plate all came from a single clone. Lederberg then exposed
one plate to lambda and noted the colonies that survived. Then,
he picked the corresponding colony on the replica plate and grew
it up. All the bacteria he grew were resistant to the phage --
even though they had never been exposed to it. In other words,
the mutation was present before its effect was needed. [2]

In 1988, Cairns questioned the experimental design of
these studies. He suggested that they did indeed show that
some mutations occured at random, but they did not rule out the
possibility that other mutations could be directed. Lambda kills
bacteria instantly, he reasoned; I'll try the experiment over
with something that will slowly kill the bacteria to see if,
given a chance, bacteria can direct their mutations. His
paper on lactose starved bacteria suggested that some mutations
were directed (i.e. the specific mutation -- and only the specific
mutation -- could be induced by the cell.) However, his study
drew lots of criticism becuase it left a lot of loose ends. [3]

In 1990, Hall released a data set that expanded on
Cairn's work and met all the earlier criticisms. He showed
that, under stress, some bacteria can induce a mutation to
fix a "broken" gene -- and not produce (many) other mutations.
In other words, the stress was not acting as generalized
mutagen. The needed mutation was occuring far too often to
be explained by random mutagenesis. [4]

The field is still divided about this topic. I'm
convinced that Hall has demonstrated a class of (seemingly)
non-random mutations. But, in interpreting the possible
impact on evolutionary theory, one must be aware of exactly
what effect has been shown and the distribution of organisms
that can be affected. The only effect shown so far is a
directed mutation rescuing a "dead" gene. Nobody has shown that
directed mutations can create a novel phenotype.

In addition, only unicellular organisms (or organisms with
totipotent cell lines) can have an evolutionary benefit from this
mode of mutation. Multicellular organisms would need the directed
mutation to occur in it's germ line cells for it to be evolutionarily
interesting; and germ line cells are the least likely to be exposed to
the stress. By the time a sperm or egg cell itself is stressed, the
multicellular organism is probably dead.

None-the-less, this is a very hot area of research. A
good description of exactly what is happening is being sought,
as well as a mechanism to explain it. Some data indicates that
there are a suite of related phenomena, for directed mutations
have been claimed to: fix single base substitutions, fix frameshift mutations and correct large insertion mutations.

In a recent paper in PNAS, Hall examined circumstances
where a bacteria needed two independent mutations in order to
survive. He concluded that, in bacteria, mutations occur more
frequently when they are needed than when they are not.

He experimented on three strains of E. Coli deficient
in the tryptophan (trp) operon. One strain contained a mutation
at position 46 of the trpA gene. The second strain contained
a mutation at position 9578 of the trpB gene and the third contained both mutations. None of the strains could produce tryptophan needed for survival or growth.

He grew up the trpA and trpB strains in media that contained trp so the mutations did not hinder their growth. Then
he spread them on petri dishes that contained all their required
nutrients except trp; so, only cells that mutated could survive
on these petri plates. He examined the plates for evidence of
growth every day for 30 days. As time went on, many revertants
for each strain arose. Hall measured the reversion rate
for both strains (trpA and trpB), and repeated the experiment
using the trpAB strain.

Now, if the reversion mutations in trpA and trpB
occured randomly, the reversion rate for trpAB should
equal the reversion rate of trpA times the reversion rate
of trpB. Hall found the rate to be 10^8 higher than this.
(Yes, that's significant 8-).

The revertants Hall found fell into three different
classes (I, II and III). Class III grew the fastest (wild
type rate), Class II grew slower and class I grew the slowest.
When he sequenced the genes in these revertants, he found that
class III revertants produced the correct mutation such that
the original amino acid was restored to trpA. Class II mutants
produced a mutation such that a similar amino acid was restored to
trpA -- making it functional enough to save the cell. In class I
mutants, no mutation was evident in trpA -- evidently a suppressor
mutation occured (a mutation in another gene, usually tRNA, to
compensate for another mutation.) In the trpB region, all the
classes had the correct mutation. No other mutations were found
in the regions sequenced. (Hall ruled out the fact that he was
selecting for bacteria with extremely high mutation rates in
another part of the paper -- see the ref if you are interested.)

So, his data indicates that the bacteria could somehow
induce the mutations they needed for survival -- and only those
mutations.

Tomorrow, or maybe Monday, I'll summarize a paper by
Cairns that demonstrates adaptive reversion mutations that
involves a frameshift mutation. I'm also preparing a post
about a new example of speciation.